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Protein

ADP-ribosylation factor-like protein 13B

Gene

ARL13B

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Cilium-specific protein required to control the microtubule-based, ciliary axoneme structure. May act by maintaining the association between IFT subcomplexes A and B. Binds GTP but is not able to hydrolyze it; the GTPase activity remains unclear. Required to pattern the neural tube. Involved in cerebral cortex development: required for the initial formation of a polarized radial glial scaffold, the first step in the construction of the cerebral cortex, by regulating ciliary signaling. Regulates the migration and placement of postmitotic interneurons in the developing cerebral cortex. May regulate endocytic recycling traffic; however, additional evidences are required to confirm these data.1 Publication

Miscellaneous

Used as a ciliary marker because of its specific localization to microtubule doublets of the ciliary axoneme.

Caution

Was initially thought to form a homodimer (PubMed:18554500). However, 3D structure of C.reinhardtii ortholog showed that it is probably not the case.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi28 – 35GTPBy similarity8
Nucleotide bindingi71 – 75GTPBy similarity5
Nucleotide bindingi130 – 133GTPBy similarity4

GO - Molecular functioni

GO - Biological processi

Keywordsi

LigandGTP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-HSA-5624958 ARL13B-mediated ciliary trafficking of INPP5E

Names & Taxonomyi

Protein namesi
Recommended name:
ADP-ribosylation factor-like protein 13B
Alternative name(s):
ADP-ribosylation factor-like protein 2-like 1
Short name:
ARL2-like protein 1
Gene namesi
Name:ARL13B
Synonyms:ARL2L1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

EuPathDBiHostDB:ENSG00000169379.15
HGNCiHGNC:25419 ARL13B
MIMi608922 gene
neXtProtiNX_Q3SXY8

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cell membrane, Cell projection, Cilium, Membrane

Pathology & Biotechi

Involvement in diseasei

Joubert syndrome 8 (JBTS8)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy and renal disease.
See also OMIM:612291
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05437179R → Q in JBTS8; reduces binding to GTP. 1 PublicationCorresponds to variant dbSNP:rs121912606EnsemblClinVar.1
Natural variantiVAR_07749686Y → C in JBTS8; the patient also manifests obesity as a feature; decreased localization to cilium. 1 PublicationCorresponds to variant dbSNP:rs863225430EnsemblClinVar.1
Natural variantiVAR_054372200R → C in JBTS8. 1 PublicationCorresponds to variant dbSNP:rs121912608EnsemblClinVar.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi35T → N: Does not affect localization to cilia. 1 Publication1
Mutagenesisi130N → I: Does not affect localization to cilia. 1 Publication1
Mutagenesisi231K → R: No effect. Abolishes sumoylation; when associated with R-270; R-275; R-276; R-279 and R-329. 1 Publication1
Mutagenesisi270K → R: No effect. Abolishes sumoylation; when associated with R-231; R-275; R-276; R-279 and R-329. 1 Publication1
Mutagenesisi275K → R: No effect. Abolishes sumoylation; when associated with R-231; R-270; R-276; R-279 and R-329. 1 Publication1
Mutagenesisi276K → R: No effect. Abolishes sumoylation; when associated with R-231; R-270; R-275; R-279 and R-329. 1 Publication1
Mutagenesisi279K → R: No effect. Abolishes sumoylation; when associated with R-231; R-270; R-275; R-276 and R-329. 1 Publication1
Mutagenesisi329K → R: Abolishes sumoylation. Abolishes sumoylation; when associated with R-231; R-270; R-275; R-276 and R-279. 1 Publication1

Keywords - Diseasei

Ciliopathy, Disease mutation, Joubert syndrome

Organism-specific databases

DisGeNETi200894
GeneReviewsiARL13B
MalaCardsiARL13B
MIMi612291 phenotype
OpenTargetsiENSG00000169379
Orphaneti475 Joubert syndrome
PharmGKBiPA134975272

Polymorphism and mutation databases

BioMutaiARL13B
DMDMi115503786

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002511371 – 428ADP-ribosylation factor-like protein 13BAdd BLAST428

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi8S-palmitoyl cysteineBy similarity1
Lipidationi9S-palmitoyl cysteineBy similarity1
Cross-linki329Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)Curated

Post-translational modificationi

Sumoylation is required for PKD2 entry into cilium.1 Publication

Keywords - PTMi

Isopeptide bond, Lipoprotein, Palmitate, Ubl conjugation

Proteomic databases

EPDiQ3SXY8
MaxQBiQ3SXY8
PaxDbiQ3SXY8
PeptideAtlasiQ3SXY8
PRIDEiQ3SXY8
ProteomicsDBi61823
61824 [Q3SXY8-2]

PTM databases

iPTMnetiQ3SXY8
PhosphoSitePlusiQ3SXY8
SwissPalmiQ3SXY8

Expressioni

Tissue specificityi

Expressed in the developing brain.1 Publication

Gene expression databases

BgeeiENSG00000169379 Expressed in 186 organ(s), highest expression level in secondary oocyte
CleanExiHS_ARL13B
ExpressionAtlasiQ3SXY8 baseline and differential
GenevisibleiQ3SXY8 HS

Organism-specific databases

HPAiHPA048926

Interactioni

Subunit structurei

Monomer (By similarity). Interacts with PIFO. Interacts with IFT complex B components IFT46 and IFT74.By similarity2 Publications

Protein-protein interaction databases

BioGridi128353, 27 interactors
IntActiQ3SXY8, 122 interactors
STRINGi9606.ENSP00000377769

Structurei

3D structure databases

ProteinModelPortaliQ3SXY8
SMRiQ3SXY8
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili192 – 245Sequence analysisAdd BLAST54

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi369 – 419Pro-richAdd BLAST51

Sequence similaritiesi

Belongs to the small GTPase superfamily. Arf family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG0074 Eukaryota
KOG0076 Eukaryota
ENOG410XRG9 LUCA
GeneTreeiENSGT00550000074639
HOGENOMiHOG000034031
HOVERGENiHBG060221
InParanoidiQ3SXY8
KOiK07962
OMAiKKGLFWL
OrthoDBiEOG091G0BQV
PhylomeDBiQ3SXY8
TreeFamiTF105476

Family and domain databases

InterProiView protein in InterPro
IPR027417 P-loop_NTPase
IPR005225 Small_GTP-bd_dom
IPR006689 Small_GTPase_ARF/SAR
PfamiView protein in Pfam
PF00025 Arf, 1 hit
PRINTSiPR00328 SAR1GTPBP
SUPFAMiSSF52540 SSF52540, 1 hit
TIGRFAMsiTIGR00231 small_GTP, 1 hit
PROSITEiView protein in PROSITE
PS51417 ARF, 1 hit

Sequences (3+)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 3 described isoforms and 2 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q3SXY8-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MFSLMASCCG WFKRWREPVR KVTLLMVGLD NAGKTATAKG IQGEYPEDVA
60 70 80 90 100
PTVGFSKINL RQGKFEVTIF DLGGGIRIRG IWKNYYAESY GVIFVVDSSD
110 120 130 140 150
EERMEETKEA MSEMLRHPRI SGKPILVLAN KQDKEGALGE ADVIECLSLE
160 170 180 190 200
KLVNEHKCLC QIEPCSAISG YGKKIDKSIK KGLYWLLHVI ARDFDALNER
210 220 230 240 250
IQKETTEQRA LEEQEKQERA ERVRKLREER KQNEQEQAEL DGTSGLAELD
260 270 280 290 300
PEPTNPFQPI ASVIIENEGK LEREKKNQKM EKDSDGCHLK HKMEHEQIET
310 320 330 340 350
QGQVNHNGQK NNEFGLVENY KEALTQQLKN EDETDRPSLE SANGKKKTKK
360 370 380 390 400
LRMKRNHRVE PLNIDDCAPE SPTPPPPPPP VGWGTPKVTR LPKLEPLGET
410 420
HHNDFYRKPL PPLAVPQRPN SDAHDVIS
Length:428
Mass (Da):48,643
Last modified:October 11, 2005 - v1
Checksum:i002B38A38D1F7BDD
GO
Isoform 2 (identifier: Q3SXY8-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     21-127: Missing.

Note: No experimental confirmation available.
Show »
Length:321
Mass (Da):36,795
Checksum:iD4D82D271E9E7F1E
GO
Isoform 3 (identifier: Q3SXY8-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-103: Missing.

Note: No experimental confirmation available.
Show »
Length:325
Mass (Da):37,087
Checksum:i21F4DA7BFC23125C
GO

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F8WAY0F8WAY0_HUMAN
ADP-ribosylation factor-like protei...
ARL13B
56Annotation score:
F8W837F8W837_HUMAN
ADP-ribosylation factor-like protei...
ARL13B
89Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti275K → KK in CAD28544 (PubMed:17974005).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05437179R → Q in JBTS8; reduces binding to GTP. 1 PublicationCorresponds to variant dbSNP:rs121912606EnsemblClinVar.1
Natural variantiVAR_07749686Y → C in JBTS8; the patient also manifests obesity as a feature; decreased localization to cilium. 1 PublicationCorresponds to variant dbSNP:rs863225430EnsemblClinVar.1
Natural variantiVAR_054372200R → C in JBTS8. 1 PublicationCorresponds to variant dbSNP:rs121912608EnsemblClinVar.1
Natural variantiVAR_048319348T → S. Corresponds to variant dbSNP:rs33944211EnsemblClinVar.1
Natural variantiVAR_069190390R → L in a nephronophthisis (NPHP) patient. 1 Publication1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0454211 – 103Missing in isoform 3. 1 PublicationAdd BLAST103
Alternative sequenceiVSP_02073321 – 127Missing in isoform 2. 1 PublicationAdd BLAST107

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL713789 mRNA Translation: CAD28544.2
AC117474 Genomic DNA No translation available.
AC130896 Genomic DNA No translation available.
CH471052 Genomic DNA Translation: EAW79897.1
CH471052 Genomic DNA Translation: EAW79901.1
CH471052 Genomic DNA Translation: EAW79898.1
BC094725 mRNA Translation: AAH94725.1
BC104035 mRNA Translation: AAI04036.1
BC104036 mRNA Translation: AAI04037.1
CCDSiCCDS2924.1 [Q3SXY8-2]
CCDS2925.1 [Q3SXY8-1]
CCDS54615.1 [Q3SXY8-3]
RefSeqiNP_001167621.1, NM_001174150.1 [Q3SXY8-1]
NP_001167622.1, NM_001174151.1 [Q3SXY8-3]
NP_659433.2, NM_144996.3 [Q3SXY8-2]
NP_878899.1, NM_182896.2 [Q3SXY8-1]
XP_016861342.1, XM_017005853.1 [Q3SXY8-3]
UniGeneiHs.533086

Genome annotation databases

EnsembliENST00000303097; ENSP00000306225; ENSG00000169379 [Q3SXY8-2]
ENST00000394222; ENSP00000377769; ENSG00000169379 [Q3SXY8-1]
ENST00000471138; ENSP00000420780; ENSG00000169379 [Q3SXY8-1]
ENST00000535334; ENSP00000445145; ENSG00000169379 [Q3SXY8-3]
GeneIDi200894
KEGGihsa:200894
UCSCiuc003drc.4 human [Q3SXY8-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL713789 mRNA Translation: CAD28544.2
AC117474 Genomic DNA No translation available.
AC130896 Genomic DNA No translation available.
CH471052 Genomic DNA Translation: EAW79897.1
CH471052 Genomic DNA Translation: EAW79901.1
CH471052 Genomic DNA Translation: EAW79898.1
BC094725 mRNA Translation: AAH94725.1
BC104035 mRNA Translation: AAI04036.1
BC104036 mRNA Translation: AAI04037.1
CCDSiCCDS2924.1 [Q3SXY8-2]
CCDS2925.1 [Q3SXY8-1]
CCDS54615.1 [Q3SXY8-3]
RefSeqiNP_001167621.1, NM_001174150.1 [Q3SXY8-1]
NP_001167622.1, NM_001174151.1 [Q3SXY8-3]
NP_659433.2, NM_144996.3 [Q3SXY8-2]
NP_878899.1, NM_182896.2 [Q3SXY8-1]
XP_016861342.1, XM_017005853.1 [Q3SXY8-3]
UniGeneiHs.533086

3D structure databases

ProteinModelPortaliQ3SXY8
SMRiQ3SXY8
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi128353, 27 interactors
IntActiQ3SXY8, 122 interactors
STRINGi9606.ENSP00000377769

PTM databases

iPTMnetiQ3SXY8
PhosphoSitePlusiQ3SXY8
SwissPalmiQ3SXY8

Polymorphism and mutation databases

BioMutaiARL13B
DMDMi115503786

Proteomic databases

EPDiQ3SXY8
MaxQBiQ3SXY8
PaxDbiQ3SXY8
PeptideAtlasiQ3SXY8
PRIDEiQ3SXY8
ProteomicsDBi61823
61824 [Q3SXY8-2]

Protocols and materials databases

DNASUi200894
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000303097; ENSP00000306225; ENSG00000169379 [Q3SXY8-2]
ENST00000394222; ENSP00000377769; ENSG00000169379 [Q3SXY8-1]
ENST00000471138; ENSP00000420780; ENSG00000169379 [Q3SXY8-1]
ENST00000535334; ENSP00000445145; ENSG00000169379 [Q3SXY8-3]
GeneIDi200894
KEGGihsa:200894
UCSCiuc003drc.4 human [Q3SXY8-1]

Organism-specific databases

CTDi200894
DisGeNETi200894
EuPathDBiHostDB:ENSG00000169379.15
GeneCardsiARL13B
GeneReviewsiARL13B
HGNCiHGNC:25419 ARL13B
HPAiHPA048926
MalaCardsiARL13B
MIMi608922 gene
612291 phenotype
neXtProtiNX_Q3SXY8
OpenTargetsiENSG00000169379
Orphaneti475 Joubert syndrome
PharmGKBiPA134975272
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0074 Eukaryota
KOG0076 Eukaryota
ENOG410XRG9 LUCA
GeneTreeiENSGT00550000074639
HOGENOMiHOG000034031
HOVERGENiHBG060221
InParanoidiQ3SXY8
KOiK07962
OMAiKKGLFWL
OrthoDBiEOG091G0BQV
PhylomeDBiQ3SXY8
TreeFamiTF105476

Enzyme and pathway databases

ReactomeiR-HSA-5624958 ARL13B-mediated ciliary trafficking of INPP5E

Miscellaneous databases

ChiTaRSiARL13B human
GeneWikiiARL13B
GenomeRNAii200894
PROiPR:Q3SXY8
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000169379 Expressed in 186 organ(s), highest expression level in secondary oocyte
CleanExiHS_ARL13B
ExpressionAtlasiQ3SXY8 baseline and differential
GenevisibleiQ3SXY8 HS

Family and domain databases

InterProiView protein in InterPro
IPR027417 P-loop_NTPase
IPR005225 Small_GTP-bd_dom
IPR006689 Small_GTPase_ARF/SAR
PfamiView protein in Pfam
PF00025 Arf, 1 hit
PRINTSiPR00328 SAR1GTPBP
SUPFAMiSSF52540 SSF52540, 1 hit
TIGRFAMsiTIGR00231 small_GTP, 1 hit
PROSITEiView protein in PROSITE
PS51417 ARF, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiAR13B_HUMAN
AccessioniPrimary (citable) accession number: Q3SXY8
Secondary accession number(s): D3DN29
, G3V1S8, Q504W8, Q8TCL5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: October 11, 2005
Last modified: November 7, 2018
This is version 119 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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